Blender 2.8 customised themes
That would be an area that could be improved.

If you change theme settings, and then press the + button next to the theme list you can give your new theme a name. By using an existing custom theme name, you can overwrite your existing theme settings. If you use an existing name of a theme that is included with blender then you get two themes with the same name.

Custom themes are saved into scripts/presets/interface_theme along with your startup and userpref files.

You could make a suggestion at Right Click Select to see if someone wants to work on making this more intuitive.